Prediction of biomarkers of oral squamous cell carcinoma using microarray technology

Abstract

Microarray data is used to screen the genes of oral squamous cell carcinoma (OSCC). Microarray data of OSCC and normal tissues were downloaded from GEO database and analyzed with Benjamini-Hochberg (BH) method. Differentially expressed genes (DEGs) were then uploaded on DAVID database to process enrichment analysis. Target genes were finally chosen for verification experiment in vitro and in vivo. 78 DEGs were selected from 54676 genes, including 46 up- and 32 down- regulation. GO term showed that these genes were related to epidermal growth (biological processes), extracellular region (cellular components) and cytokines activity (molecular function). Protein network interaction demonstrated that OSCC was closely allied to the five key genes including CXCL10, IFI6, IFI27, ADAMTS2 and COL5A1, which was consistent with the RT-PCR data. High-expressed gene CXCL10 was chosen for further cell experiment, and the results indicated that CXCL10 can promote the proliferation, migration and invasion of normal cells and inhibited the cancer cells after si-RNA transfection. Moreover, it has been proven that CXCL10 was possibly related to the occurrence and development of OSCC. Understanding the regulation of OSCC expression will shed light on the screening of cancer biomarker.

Pathway based prognostic gene expression profile of buccal and gingivo‐buccal oral squamous cell carcinoma in smokeless tobacco chewers

“…The mechanism of IL1B‐triggered OSCC proliferation on OSCC cell lines was studied; it was found that IL1B transactivates epidermal growth factor via the CXCL1‐CXCR2 axis . A study using microarray technology to predict OSCC biomarkers identified high expression of CXCL10 which has been related to OSCC occurrence and development and suggested its use as a novel diagnostic marker . CXCL1, CXCL8, and CXCL10 were upregulated in the present study.…”

“…Of late, many studies have utilized high‐throughput microarray technology to identify the carcinogenic process and to relate gene expression signatures to clinical outcomes . However, to date, there are no molecular markers that are used clinically to stratify patients with OSCC.…”

“…Of late, many studies have utilized high-throughput microarray technology to identify the carcinogenic process and to relate gene expression signatures to clinical outcomes. [6][7][8] However, to date, there are no molecular markers that are used clinically to stratify patients with OSCC. This is probably because microarray technology is inadequate to characterize multiple transcripts of genes in the complex human transcriptome.…”

Assessment of cellular and serum proteome from tongue squamous cell carcinoma patient lacking addictive proclivities for tobacco, betel nut, and alcohol: Case study

“…The novel truncated C‐terminus (N‐terminus lacking) secretory isoform of DNAJC13 with potential prognostic and/or diagnostic applicability, has been named as “ Bhuley_Ram_Oral_Cancer_protein_truncated DNAJC13 ” or “ BROCP_tDNAJC13 .” The TCGA study (the most comprehensive work on head and neck squamous cell carcinoma associated genomic alterations) has reported alterations in numerous genes including SSFA2 , GIPC2 , DNAJC13 , KRT1 , SCCA1 ( SERPINB3 ); 11 MRPL genes namely MRPL1 , MRPL2 , MRPL15 , MRPL21 , MRPL27 , MRPL28 , MRPL36 , MRPL37 , MRPL41 , MRPL50 , MRPL52 and 18 c7orfs namely C7orf4, C7orf10, C7orf13, C7orf16, C7orf23, C7orf28B, C7orf34, C7orf42, C7orf44, C7orf45, C7orf46, C7orf58, C7orf60, C7orf63, C7orf66, C7orf69, C7orf70, and C7orf72 . Many, microarray based experimental studies have fished out numerous genes involved in OSCC pathology . The identification of crucial genes along with their expressional and regulatory behaviors under normal and diseased physiologies is quintessential for understanding the molecular pathways involved in acute and chronic disorders of oral mucosa and there correlation with the low to high severities at the histological levels.…”

Improving accuracy of RNA-based diagnosis and prognosis of oral cancer by using noninvasive methods

“…Well over a decade ago the first studies were published that attempted to allow the identification of head and neck and, more narrowly, oral squamous cell carcinoma (OSCC) based on gene expression [1–3]. These studies relied on surgical biopsy to obtain tissue from which RNA was purified then analyzed.…”